Re: amber-developers: PIMD, NEB, LES - request for code inspection and tests

From: Carlos Simmerling <>
Date: Fri, 20 Jul 2007 18:28:16 -0400

I think this is because all of the LES test cases were created
before pimd or neb existed, and then both of those used LES
parts of the code to run pimd/neb.

I've been working on some major changes to neb anyway,
following what has already been done to put neb into multisander.
does anyone want to keep neb in the LES style, or can we make it
multisander only?

On 7/20/07, Scott Brozell <> wrote:
> Hi,
> I have just committed a bug fix in subroutine do_pme_recip
> to prevent a seg fault in test/LES/Run.PME_LES.
> Also I have just added pimd initialization when ineb > 0.
> These should be carefully examined because the interplay between
> pimd, neb, and les is not clear to me.
> My cvs logs for ew_force.f and sander.f
> are detailed and raise several issues.
> In addition, updated documentation and detailed comments seem to be
> lacking. Furthermore, we need more test cases for these features;
> think out of the box; for example, there are no test cases in LES
> for ineb > 0 even though code paths for such exist.
> thanks,
> Scott

Carlos L. Simmerling, Ph.D.
Associate Professor                 Phone: (631) 632-1336
Center for Structural Biology       Fax:   (631) 632-1555
CMM Bldg, Room G80
Stony Brook University              E-mail:
Stony Brook, NY 11794-5115          Web:
Received on Sun Jul 22 2007 - 06:07:52 PDT
Custom Search